# User:Hussein Alasadi/Notebook/stephens/2013/10/16

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 Revision as of 00:04, 17 October 2013 (view source) (Autocreate 2013/10/16 Entry for User:Hussein_Alasadi/Notebook/stephens)← Previous diff Current revision (13:33, 17 October 2013) (view source) (→Simulating evolution and then pooled sequencing) (11 intermediate revisions not shown.) Line 6: Line 6: | colspan="2"| | colspan="2"| - ==Entry title== + ==Simulating evolution and then pooled sequencing== - * Insert content here... + + * '''We start with a population of N individuals with a SNP distribution $P(M)$ ~ $N(\mu, \Sigma)$.''' + We can use Dick Hudson's MsSel (MS with selection) to generate a SNP distribution. + + + * '''We then evolve the populations for g generations with selection for SNP j''' + In MsSel, we can specify an allele frequency trajectory for a site. We can generate a trajectory based on a simple W-F simulation with selection. + + + Or, we may have to use [http://arxiv.org/abs/1310.3234 forqs]. + + + * '''Simulate pooled sequencing''' + + (1) draw a coverage (n) from $Pois(\lambda)$ where $\lambda \approx 40-50$ + + (2) $f_i$ (frequency of the ith SNP) ~ $B(n, f_i^{true})$ +

## Current revision

Analyzing pooled sequenced data with selection Main project page
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## Simulating evolution and then pooled sequencing

• We start with a population of N individuals with a SNP distribution P(M) ~ N(μ,Σ).

We can use Dick Hudson's MsSel (MS with selection) to generate a SNP distribution.

• We then evolve the populations for g generations with selection for SNP j

In MsSel, we can specify an allele frequency trajectory for a site. We can generate a trajectory based on a simple W-F simulation with selection.

Or, we may have to use forqs.

• Simulate pooled sequencing

(1) draw a coverage (n) from Pois(λ) where $\lambda \approx 40-50$

(2) fi (frequency of the ith SNP) ~ $B(n, f_i^{true})$